I read an interesting article this weekend about lopsided bootbanks in ESXi and as Kyle states, the impact of this is very minor. If you would like to check to see if you would be impacted by this and remediate prior to upgrading from ESXi 4.x to 5.x, you can use the following vSphere SDK for Perl script findLopsidedBootbanks.pl which was modified from an existing script (queryDiskParition.pl) that allows you to query for partitions on a disk.
Note: Remediation is only necessary if you plan on using VUM (Update Manager) to upgrade from ESXi 3.x/4.x to 5.x as it expects both bootbanks to be the same size, else a scripted install/upgrade will extend bootbank1 and ensure it matches bootbank2 size.
Here is an ESXi 3.5 host that was directly upgraded to ESXi 4.0 and as you can see from the partition layout, bootbank1 (partition 5) and bootbank2 (partition 6) differ in size.
Using the findLopsidedBootbanks.pl you can connect to either vCenter server or directly to an ESXi host and it will check to see if there are any lopsided bootbanks.
Download: findLopsidedBootbanks.pl script here.